Multiple sequence alignment - TraesCS5B01G203800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G203800 chr5B 100.000 4262 0 0 1 4262 371791010 371786749 0.000000e+00 7871.0
1 TraesCS5B01G203800 chr5B 78.745 701 95 39 3497 4177 371773898 371773232 1.830000e-113 420.0
2 TraesCS5B01G203800 chr5D 84.781 2188 136 83 2175 4262 320411097 320409007 0.000000e+00 2013.0
3 TraesCS5B01G203800 chr5D 91.413 1444 51 33 723 2146 320412482 320411092 0.000000e+00 1912.0
4 TraesCS5B01G203800 chr5D 90.157 508 28 9 68 569 320413134 320412643 3.590000e-180 641.0
5 TraesCS5B01G203800 chr5D 77.966 708 94 42 3497 4177 320405901 320405229 1.860000e-103 387.0
6 TraesCS5B01G203800 chr5D 97.917 48 1 0 1 48 320413164 320413117 2.730000e-12 84.2
7 TraesCS5B01G203800 chr5A 89.463 968 40 17 723 1683 413845028 413845940 0.000000e+00 1166.0
8 TraesCS5B01G203800 chr5A 91.680 637 41 9 3184 3813 413847332 413847963 0.000000e+00 872.0
9 TraesCS5B01G203800 chr5A 83.123 794 68 36 2428 3176 413846523 413847295 0.000000e+00 664.0
10 TraesCS5B01G203800 chr5A 87.175 577 44 19 68 618 413844410 413844982 2.800000e-176 628.0
11 TraesCS5B01G203800 chr5A 86.327 373 39 6 1732 2095 413845950 413846319 3.090000e-106 396.0
12 TraesCS5B01G203800 chr5A 89.404 151 6 3 3861 4011 413847964 413848104 9.410000e-42 182.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G203800 chr5B 371786749 371791010 4261 True 7871.000000 7871 100.0000 1 4262 1 chr5B.!!$R2 4261
1 TraesCS5B01G203800 chr5B 371773232 371773898 666 True 420.000000 420 78.7450 3497 4177 1 chr5B.!!$R1 680
2 TraesCS5B01G203800 chr5D 320405229 320413164 7935 True 1007.440000 2013 88.4468 1 4262 5 chr5D.!!$R1 4261
3 TraesCS5B01G203800 chr5A 413844410 413848104 3694 False 651.333333 1166 87.8620 68 4011 6 chr5A.!!$F1 3943

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
781 856 0.102300 GAAAGAGAGAGCCTCCGAGC 59.898 60.0 0.0 0.0 42.97 5.03 F
2152 2264 0.036732 TTGACCTCCCACTGCATCAC 59.963 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2688 2859 0.098200 CGAATCGTACTCGCCTGTCA 59.902 55.0 0.0 0.0 36.96 3.58 R
3658 3908 0.031178 ACGGCTCGTGAAACTACGTT 59.969 50.0 0.0 0.0 44.06 3.99 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.056092 TGCTTTGCACATTGATGTTTGA 57.944 36.364 0.00 0.00 39.39 2.69
32 33 4.633175 TGCTTTGCACATTGATGTTTGAT 58.367 34.783 0.00 0.00 39.39 2.57
33 34 4.449405 TGCTTTGCACATTGATGTTTGATG 59.551 37.500 0.00 0.00 39.39 3.07
34 35 4.449743 GCTTTGCACATTGATGTTTGATGT 59.550 37.500 0.00 0.00 39.39 3.06
35 36 5.049954 GCTTTGCACATTGATGTTTGATGTT 60.050 36.000 0.00 0.00 39.39 2.71
36 37 6.145858 GCTTTGCACATTGATGTTTGATGTTA 59.854 34.615 0.00 0.00 39.39 2.41
37 38 7.307278 GCTTTGCACATTGATGTTTGATGTTAA 60.307 33.333 0.00 0.00 39.39 2.01
38 39 7.405469 TTGCACATTGATGTTTGATGTTAAC 57.595 32.000 0.00 0.00 39.39 2.01
39 40 6.510536 TGCACATTGATGTTTGATGTTAACA 58.489 32.000 11.41 11.41 39.39 2.41
40 41 6.420306 TGCACATTGATGTTTGATGTTAACAC 59.580 34.615 11.22 5.88 39.39 3.32
41 42 6.642131 GCACATTGATGTTTGATGTTAACACT 59.358 34.615 11.22 0.12 39.39 3.55
42 43 7.169645 GCACATTGATGTTTGATGTTAACACTT 59.830 33.333 11.22 0.00 39.39 3.16
43 44 9.676195 CACATTGATGTTTGATGTTAACACTTA 57.324 29.630 11.22 0.00 39.39 2.24
44 45 9.677567 ACATTGATGTTTGATGTTAACACTTAC 57.322 29.630 11.22 7.61 37.90 2.34
45 46 9.897744 CATTGATGTTTGATGTTAACACTTACT 57.102 29.630 11.22 0.00 38.23 2.24
48 49 9.944663 TGATGTTTGATGTTAACACTTACTTTC 57.055 29.630 11.22 3.29 38.23 2.62
49 50 9.944663 GATGTTTGATGTTAACACTTACTTTCA 57.055 29.630 11.22 6.08 38.23 2.69
50 51 9.730420 ATGTTTGATGTTAACACTTACTTTCAC 57.270 29.630 11.22 0.00 38.23 3.18
51 52 8.185505 TGTTTGATGTTAACACTTACTTTCACC 58.814 33.333 11.22 3.33 30.96 4.02
52 53 6.870971 TGATGTTAACACTTACTTTCACCC 57.129 37.500 11.22 0.00 0.00 4.61
53 54 5.467399 TGATGTTAACACTTACTTTCACCCG 59.533 40.000 11.22 0.00 0.00 5.28
54 55 3.560896 TGTTAACACTTACTTTCACCCGC 59.439 43.478 3.59 0.00 0.00 6.13
55 56 2.335316 AACACTTACTTTCACCCGCA 57.665 45.000 0.00 0.00 0.00 5.69
56 57 2.335316 ACACTTACTTTCACCCGCAA 57.665 45.000 0.00 0.00 0.00 4.85
57 58 2.645802 ACACTTACTTTCACCCGCAAA 58.354 42.857 0.00 0.00 0.00 3.68
58 59 3.018149 ACACTTACTTTCACCCGCAAAA 58.982 40.909 0.00 0.00 0.00 2.44
59 60 3.444388 ACACTTACTTTCACCCGCAAAAA 59.556 39.130 0.00 0.00 0.00 1.94
163 167 1.427368 TGGCTTGGAAACCATGGTACT 59.573 47.619 20.12 8.66 31.53 2.73
260 276 2.472695 TAGGCTGCAAACAAGATCGT 57.527 45.000 0.50 0.00 0.00 3.73
310 326 6.684555 CACAATCGAGATAAAAAGTAAGCAGC 59.315 38.462 0.00 0.00 0.00 5.25
352 368 3.257127 GGAGCTCATGAGTAGTATCCACC 59.743 52.174 23.38 9.34 0.00 4.61
354 370 2.608261 GCTCATGAGTAGTATCCACCGC 60.608 54.545 23.38 1.81 0.00 5.68
355 371 2.887783 CTCATGAGTAGTATCCACCGCT 59.112 50.000 14.95 0.00 0.00 5.52
363 380 5.383476 AGTAGTATCCACCGCTATAACACT 58.617 41.667 0.00 0.00 0.00 3.55
558 585 7.148606 TGTGATACATAAACCGTACGGAAAAAG 60.149 37.037 39.52 25.58 38.96 2.27
559 586 6.873076 TGATACATAAACCGTACGGAAAAAGT 59.127 34.615 39.52 29.10 38.96 2.66
562 589 6.429624 ACATAAACCGTACGGAAAAAGTTTC 58.570 36.000 39.52 0.00 38.96 2.78
563 590 4.961435 AAACCGTACGGAAAAAGTTTCA 57.039 36.364 39.52 0.00 38.96 2.69
564 591 5.503662 AAACCGTACGGAAAAAGTTTCAT 57.496 34.783 39.52 10.68 38.96 2.57
603 665 5.064325 AGCGTACAAAAAGGAATACGGATTC 59.936 40.000 12.23 12.23 40.51 2.52
618 681 5.277601 ACGGATTCACGACATTTGTTAAG 57.722 39.130 0.00 0.00 37.61 1.85
619 682 4.753107 ACGGATTCACGACATTTGTTAAGT 59.247 37.500 0.00 0.00 37.61 2.24
621 684 6.128742 ACGGATTCACGACATTTGTTAAGTAC 60.129 38.462 0.00 0.00 37.61 2.73
623 686 7.453838 GGATTCACGACATTTGTTAAGTACTC 58.546 38.462 0.00 0.00 0.00 2.59
624 687 6.774354 TTCACGACATTTGTTAAGTACTCC 57.226 37.500 0.00 0.00 0.00 3.85
628 691 8.308931 TCACGACATTTGTTAAGTACTCCTAAT 58.691 33.333 0.00 0.00 0.00 1.73
662 730 2.973694 TAGACAATGGGAACGCCTAC 57.026 50.000 0.00 0.00 0.00 3.18
663 731 0.981183 AGACAATGGGAACGCCTACA 59.019 50.000 0.00 0.00 0.00 2.74
665 733 1.737793 GACAATGGGAACGCCTACAAG 59.262 52.381 0.00 0.00 0.00 3.16
666 734 1.073284 ACAATGGGAACGCCTACAAGT 59.927 47.619 0.00 0.00 0.00 3.16
667 735 2.159382 CAATGGGAACGCCTACAAGTT 58.841 47.619 0.00 0.00 0.00 2.66
696 771 4.049393 GGAACGCTGTGTGCTCTT 57.951 55.556 0.00 0.00 40.11 2.85
697 772 2.321213 GGAACGCTGTGTGCTCTTT 58.679 52.632 0.00 0.00 40.11 2.52
698 773 0.663153 GGAACGCTGTGTGCTCTTTT 59.337 50.000 0.00 0.00 40.11 2.27
699 774 1.065551 GGAACGCTGTGTGCTCTTTTT 59.934 47.619 0.00 0.00 40.11 1.94
700 775 2.289547 GGAACGCTGTGTGCTCTTTTTA 59.710 45.455 0.00 0.00 40.11 1.52
701 776 3.545633 GAACGCTGTGTGCTCTTTTTAG 58.454 45.455 0.00 0.00 40.11 1.85
702 777 2.561569 ACGCTGTGTGCTCTTTTTAGT 58.438 42.857 0.00 0.00 40.11 2.24
703 778 2.544267 ACGCTGTGTGCTCTTTTTAGTC 59.456 45.455 0.00 0.00 40.11 2.59
704 779 2.410262 CGCTGTGTGCTCTTTTTAGTCG 60.410 50.000 0.00 0.00 40.11 4.18
705 780 2.544267 GCTGTGTGCTCTTTTTAGTCGT 59.456 45.455 0.00 0.00 38.95 4.34
706 781 3.739300 GCTGTGTGCTCTTTTTAGTCGTA 59.261 43.478 0.00 0.00 38.95 3.43
707 782 4.143305 GCTGTGTGCTCTTTTTAGTCGTAG 60.143 45.833 0.00 0.00 38.95 3.51
708 783 4.940463 TGTGTGCTCTTTTTAGTCGTAGT 58.060 39.130 0.00 0.00 0.00 2.73
709 784 6.075762 TGTGTGCTCTTTTTAGTCGTAGTA 57.924 37.500 0.00 0.00 0.00 1.82
710 785 6.684686 TGTGTGCTCTTTTTAGTCGTAGTAT 58.315 36.000 0.00 0.00 0.00 2.12
711 786 6.584942 TGTGTGCTCTTTTTAGTCGTAGTATG 59.415 38.462 0.00 0.00 0.00 2.39
712 787 6.034683 GTGTGCTCTTTTTAGTCGTAGTATGG 59.965 42.308 0.00 0.00 0.00 2.74
713 788 5.005490 GTGCTCTTTTTAGTCGTAGTATGGC 59.995 44.000 0.00 0.00 0.00 4.40
714 789 5.107133 GCTCTTTTTAGTCGTAGTATGGCA 58.893 41.667 0.00 0.00 0.00 4.92
715 790 5.579511 GCTCTTTTTAGTCGTAGTATGGCAA 59.420 40.000 0.00 0.00 0.00 4.52
716 791 6.455246 GCTCTTTTTAGTCGTAGTATGGCAAC 60.455 42.308 0.00 0.00 0.00 4.17
734 809 1.290955 CAGTAGCCAACCGAACGGA 59.709 57.895 20.14 0.00 38.96 4.69
762 837 3.887621 TTGAGTATTTGACCCCGAGAG 57.112 47.619 0.00 0.00 0.00 3.20
764 839 3.437213 TGAGTATTTGACCCCGAGAGAA 58.563 45.455 0.00 0.00 0.00 2.87
779 854 1.283613 AGAGAAAGAGAGAGCCTCCGA 59.716 52.381 0.00 0.00 42.97 4.55
780 855 1.676006 GAGAAAGAGAGAGCCTCCGAG 59.324 57.143 0.00 0.00 42.97 4.63
781 856 0.102300 GAAAGAGAGAGCCTCCGAGC 59.898 60.000 0.00 0.00 42.97 5.03
782 857 0.613292 AAAGAGAGAGCCTCCGAGCA 60.613 55.000 0.00 0.00 42.97 4.26
783 858 1.037030 AAGAGAGAGCCTCCGAGCAG 61.037 60.000 0.00 0.00 42.97 4.24
827 906 1.596895 GCTCTCCGTTTCCCTCTCGT 61.597 60.000 0.00 0.00 0.00 4.18
970 1055 2.268280 CTGGGCAGCCAGACAGAG 59.732 66.667 15.19 0.00 39.96 3.35
972 1057 2.241479 CTGGGCAGCCAGACAGAGAG 62.241 65.000 15.19 0.00 39.96 3.20
977 1062 4.154347 GCCAGACAGAGAGGGCGG 62.154 72.222 0.00 0.00 36.58 6.13
980 1065 1.515020 CAGACAGAGAGGGCGGAAG 59.485 63.158 0.00 0.00 0.00 3.46
1511 1605 0.107993 CGGCTGATGAAGGAGAGCAA 60.108 55.000 0.00 0.00 32.83 3.91
1635 1732 1.009675 GCTGTGCACCAACAAGACG 60.010 57.895 15.69 0.00 0.00 4.18
1783 1890 4.096003 CATGCGAACCCCCTCCGT 62.096 66.667 0.00 0.00 0.00 4.69
1832 1939 0.249741 GGACGTCCCAATCCCATACG 60.250 60.000 24.75 0.00 39.37 3.06
1870 1977 2.757508 TCTGCTCTGCTCCTCCCG 60.758 66.667 0.00 0.00 0.00 5.14
1948 2059 4.513442 TCTGTCCAGATTCCCGTTTTATG 58.487 43.478 0.00 0.00 31.41 1.90
2006 2118 1.024271 AACGGAATGGATTGGATGCG 58.976 50.000 0.00 0.00 0.00 4.73
2026 2138 2.095461 GGAGTGGATCTTTCTTTGCCC 58.905 52.381 0.00 0.00 0.00 5.36
2139 2251 0.106918 TTGGCACGTCCTTTTGACCT 60.107 50.000 0.00 0.00 41.18 3.85
2140 2252 0.534203 TGGCACGTCCTTTTGACCTC 60.534 55.000 5.77 0.00 41.18 3.85
2141 2253 1.235281 GGCACGTCCTTTTGACCTCC 61.235 60.000 0.00 0.00 41.18 4.30
2142 2254 1.235281 GCACGTCCTTTTGACCTCCC 61.235 60.000 0.00 0.00 41.18 4.30
2143 2255 0.107831 CACGTCCTTTTGACCTCCCA 59.892 55.000 0.00 0.00 41.18 4.37
2144 2256 0.108019 ACGTCCTTTTGACCTCCCAC 59.892 55.000 0.00 0.00 41.18 4.61
2145 2257 0.396811 CGTCCTTTTGACCTCCCACT 59.603 55.000 0.00 0.00 41.18 4.00
2146 2258 1.878102 CGTCCTTTTGACCTCCCACTG 60.878 57.143 0.00 0.00 41.18 3.66
2147 2259 0.110486 TCCTTTTGACCTCCCACTGC 59.890 55.000 0.00 0.00 0.00 4.40
2148 2260 0.178992 CCTTTTGACCTCCCACTGCA 60.179 55.000 0.00 0.00 0.00 4.41
2149 2261 1.548582 CCTTTTGACCTCCCACTGCAT 60.549 52.381 0.00 0.00 0.00 3.96
2150 2262 1.815003 CTTTTGACCTCCCACTGCATC 59.185 52.381 0.00 0.00 0.00 3.91
2151 2263 0.770499 TTTGACCTCCCACTGCATCA 59.230 50.000 0.00 0.00 0.00 3.07
2152 2264 0.036732 TTGACCTCCCACTGCATCAC 59.963 55.000 0.00 0.00 0.00 3.06
2153 2265 1.078143 GACCTCCCACTGCATCACC 60.078 63.158 0.00 0.00 0.00 4.02
2154 2266 1.841302 GACCTCCCACTGCATCACCA 61.841 60.000 0.00 0.00 0.00 4.17
2155 2267 1.077930 CCTCCCACTGCATCACCAG 60.078 63.158 0.00 0.00 38.78 4.00
2156 2268 1.748122 CTCCCACTGCATCACCAGC 60.748 63.158 0.00 0.00 36.29 4.85
2157 2269 2.194388 CTCCCACTGCATCACCAGCT 62.194 60.000 0.00 0.00 36.29 4.24
2158 2270 1.748122 CCCACTGCATCACCAGCTC 60.748 63.158 0.00 0.00 36.29 4.09
2159 2271 2.104859 CCACTGCATCACCAGCTCG 61.105 63.158 0.00 0.00 36.29 5.03
2160 2272 1.375140 CACTGCATCACCAGCTCGT 60.375 57.895 0.00 0.00 36.29 4.18
2161 2273 1.375140 ACTGCATCACCAGCTCGTG 60.375 57.895 4.93 4.93 36.29 4.35
2169 2281 2.126071 CCAGCTCGTGGTACGTGG 60.126 66.667 0.00 0.00 43.14 4.94
2170 2282 2.126071 CAGCTCGTGGTACGTGGG 60.126 66.667 0.00 0.00 43.14 4.61
2171 2283 4.065281 AGCTCGTGGTACGTGGGC 62.065 66.667 0.00 0.00 43.14 5.36
2212 2324 4.493049 GTTGCCCGCCCCCGATAA 62.493 66.667 0.00 0.00 36.29 1.75
2286 2404 3.367321 GTGAAGCTTCTCCTACCCTACT 58.633 50.000 26.09 0.00 0.00 2.57
2287 2405 4.534797 GTGAAGCTTCTCCTACCCTACTA 58.465 47.826 26.09 0.00 0.00 1.82
2289 2407 4.017775 TGAAGCTTCTCCTACCCTACTACA 60.018 45.833 26.09 0.00 0.00 2.74
2290 2408 3.900971 AGCTTCTCCTACCCTACTACAC 58.099 50.000 0.00 0.00 0.00 2.90
2297 2415 2.784682 CCTACCCTACTACACCTCCTCT 59.215 54.545 0.00 0.00 0.00 3.69
2302 2420 2.025226 CCTACTACACCTCCTCTGTCCA 60.025 54.545 0.00 0.00 0.00 4.02
2304 2422 3.191888 ACTACACCTCCTCTGTCCATT 57.808 47.619 0.00 0.00 0.00 3.16
2323 2444 1.578897 TCCATCATTCACCCGGAGAA 58.421 50.000 0.73 7.49 0.00 2.87
2326 2447 2.283298 CATCATTCACCCGGAGAACAG 58.717 52.381 0.73 3.91 0.00 3.16
2343 2477 4.754570 GAGCATCTGCATCTCGCT 57.245 55.556 4.79 0.00 45.16 4.93
2404 2542 4.357947 TGGCGACCACGTGAGCTC 62.358 66.667 19.30 6.82 41.98 4.09
2407 2545 4.039357 CGACCACGTGAGCTCGGT 62.039 66.667 19.30 10.43 34.94 4.69
2408 2546 2.430921 GACCACGTGAGCTCGGTG 60.431 66.667 23.62 23.62 34.94 4.94
2409 2547 3.208884 GACCACGTGAGCTCGGTGT 62.209 63.158 26.46 18.30 34.94 4.16
2410 2548 2.029073 CCACGTGAGCTCGGTGTT 59.971 61.111 26.46 2.85 34.94 3.32
2411 2549 1.287815 CCACGTGAGCTCGGTGTTA 59.712 57.895 26.46 1.48 34.94 2.41
2412 2550 0.732880 CCACGTGAGCTCGGTGTTAG 60.733 60.000 26.46 14.05 34.94 2.34
2413 2551 0.039437 CACGTGAGCTCGGTGTTAGT 60.039 55.000 22.74 7.76 34.94 2.24
2414 2552 0.039437 ACGTGAGCTCGGTGTTAGTG 60.039 55.000 9.64 0.00 34.94 2.74
2415 2553 0.732880 CGTGAGCTCGGTGTTAGTGG 60.733 60.000 9.64 0.00 0.00 4.00
2416 2554 0.317479 GTGAGCTCGGTGTTAGTGGT 59.683 55.000 9.64 0.00 0.00 4.16
2417 2555 1.542915 GTGAGCTCGGTGTTAGTGGTA 59.457 52.381 9.64 0.00 0.00 3.25
2418 2556 1.816835 TGAGCTCGGTGTTAGTGGTAG 59.183 52.381 9.64 0.00 0.00 3.18
2419 2557 2.089980 GAGCTCGGTGTTAGTGGTAGA 58.910 52.381 0.00 0.00 0.00 2.59
2420 2558 2.490903 GAGCTCGGTGTTAGTGGTAGAA 59.509 50.000 0.00 0.00 0.00 2.10
2421 2559 2.492484 AGCTCGGTGTTAGTGGTAGAAG 59.508 50.000 0.00 0.00 0.00 2.85
2422 2560 2.416972 GCTCGGTGTTAGTGGTAGAAGG 60.417 54.545 0.00 0.00 0.00 3.46
2423 2561 2.165845 CTCGGTGTTAGTGGTAGAAGGG 59.834 54.545 0.00 0.00 0.00 3.95
2424 2562 1.206371 CGGTGTTAGTGGTAGAAGGGG 59.794 57.143 0.00 0.00 0.00 4.79
2425 2563 1.558294 GGTGTTAGTGGTAGAAGGGGG 59.442 57.143 0.00 0.00 0.00 5.40
2465 2606 2.572104 ACTTGGCTCCAACCCTAACTAG 59.428 50.000 0.00 0.00 0.00 2.57
2553 2702 3.377346 AGGTGATGTGATTAGCTAGCG 57.623 47.619 9.55 0.00 0.00 4.26
2554 2703 2.959030 AGGTGATGTGATTAGCTAGCGA 59.041 45.455 9.55 0.00 0.00 4.93
2555 2704 3.005261 AGGTGATGTGATTAGCTAGCGAG 59.995 47.826 9.55 0.00 0.00 5.03
2685 2856 2.983791 GCCCCGTGCTGTAGGTTA 59.016 61.111 0.00 0.00 36.87 2.85
2688 2859 1.120530 CCCCGTGCTGTAGGTTAGAT 58.879 55.000 0.00 0.00 0.00 1.98
2689 2860 1.202533 CCCCGTGCTGTAGGTTAGATG 60.203 57.143 0.00 0.00 0.00 2.90
2690 2861 1.754803 CCCGTGCTGTAGGTTAGATGA 59.245 52.381 0.00 0.00 0.00 2.92
2691 2862 2.481449 CCCGTGCTGTAGGTTAGATGAC 60.481 54.545 0.00 0.00 0.00 3.06
2692 2863 2.165641 CCGTGCTGTAGGTTAGATGACA 59.834 50.000 0.00 0.00 0.00 3.58
2693 2864 3.439293 CGTGCTGTAGGTTAGATGACAG 58.561 50.000 0.00 0.00 41.82 3.51
2694 2865 3.735208 CGTGCTGTAGGTTAGATGACAGG 60.735 52.174 3.31 0.00 39.76 4.00
2698 2869 2.688446 TGTAGGTTAGATGACAGGCGAG 59.312 50.000 0.00 0.00 0.00 5.03
2699 2870 1.853963 AGGTTAGATGACAGGCGAGT 58.146 50.000 0.00 0.00 0.00 4.18
2702 2873 2.541178 GGTTAGATGACAGGCGAGTACG 60.541 54.545 0.00 0.00 42.93 3.67
2703 2874 2.320745 TAGATGACAGGCGAGTACGA 57.679 50.000 0.00 0.00 42.66 3.43
2704 2875 1.681538 AGATGACAGGCGAGTACGAT 58.318 50.000 0.00 0.00 42.66 3.73
2705 2876 2.025155 AGATGACAGGCGAGTACGATT 58.975 47.619 0.00 0.00 42.66 3.34
2706 2877 2.033550 AGATGACAGGCGAGTACGATTC 59.966 50.000 0.00 0.00 42.66 2.52
2708 2879 0.591741 GACAGGCGAGTACGATTCGG 60.592 60.000 11.29 0.00 42.66 4.30
2709 2880 1.028330 ACAGGCGAGTACGATTCGGA 61.028 55.000 11.29 0.00 42.66 4.55
2710 2881 0.099968 CAGGCGAGTACGATTCGGAA 59.900 55.000 11.29 0.00 42.66 4.30
2711 2882 1.030457 AGGCGAGTACGATTCGGAAT 58.970 50.000 11.29 2.19 42.66 3.01
2712 2883 1.129326 GGCGAGTACGATTCGGAATG 58.871 55.000 8.18 3.58 42.66 2.67
2713 2884 1.268896 GGCGAGTACGATTCGGAATGA 60.269 52.381 8.18 0.00 42.66 2.57
2714 2885 2.044860 GCGAGTACGATTCGGAATGAG 58.955 52.381 8.18 4.73 42.66 2.90
2715 2886 2.044860 CGAGTACGATTCGGAATGAGC 58.955 52.381 8.18 0.00 42.66 4.26
2717 2888 3.707793 GAGTACGATTCGGAATGAGCTT 58.292 45.455 8.18 0.00 0.00 3.74
2718 2889 3.448686 AGTACGATTCGGAATGAGCTTG 58.551 45.455 8.18 0.00 0.00 4.01
2719 2890 2.386661 ACGATTCGGAATGAGCTTGT 57.613 45.000 8.18 0.00 0.00 3.16
2720 2891 3.520290 ACGATTCGGAATGAGCTTGTA 57.480 42.857 8.18 0.00 0.00 2.41
2721 2892 4.060038 ACGATTCGGAATGAGCTTGTAT 57.940 40.909 8.18 0.00 0.00 2.29
2722 2893 5.196341 ACGATTCGGAATGAGCTTGTATA 57.804 39.130 8.18 0.00 0.00 1.47
2723 2894 5.223382 ACGATTCGGAATGAGCTTGTATAG 58.777 41.667 8.18 0.00 0.00 1.31
2751 2922 5.402398 TCATTGTATAGCTGATCCGAATCG 58.598 41.667 0.00 0.00 34.39 3.34
2752 2923 3.217599 TGTATAGCTGATCCGAATCGC 57.782 47.619 0.00 0.00 34.39 4.58
2801 2972 0.179189 CTGCTTCCGGCGACATTTTC 60.179 55.000 9.30 0.00 45.43 2.29
2823 2995 4.156556 TCCTGCAAAATCATGAGCTTGTAC 59.843 41.667 16.70 6.07 0.00 2.90
2858 3030 1.228894 TCTCCACGTCTTGGGCTCT 60.229 57.895 0.00 0.00 46.92 4.09
2860 3032 0.390472 CTCCACGTCTTGGGCTCTTC 60.390 60.000 0.00 0.00 46.92 2.87
2864 3036 1.807573 CGTCTTGGGCTCTTCGCTC 60.808 63.158 0.00 0.00 40.51 5.03
2870 3042 3.834732 GGGCTCTTCGCTCAACTTA 57.165 52.632 0.00 0.00 39.60 2.24
2882 3054 3.300066 CGCTCAACTTAACGTACTGCTAC 59.700 47.826 0.00 0.00 0.00 3.58
2888 3064 7.743104 TCAACTTAACGTACTGCTACTAGTAC 58.257 38.462 0.00 6.10 46.02 2.73
2912 3088 5.030147 TGGTAGTTTAGTCCTGATGACCAT 58.970 41.667 0.00 0.00 45.68 3.55
2964 3140 4.044426 ACGAACGTAGGTTGTTAGTGTTC 58.956 43.478 5.36 0.00 36.24 3.18
2975 3173 5.106475 GGTTGTTAGTGTTCAATTATCGCCA 60.106 40.000 0.00 0.00 0.00 5.69
2977 3175 4.094294 TGTTAGTGTTCAATTATCGCCAGC 59.906 41.667 0.00 0.00 0.00 4.85
2981 3179 3.023119 TGTTCAATTATCGCCAGCCATT 58.977 40.909 0.00 0.00 0.00 3.16
3160 3362 0.183731 ATTCCGAGGCCCCAGAAATC 59.816 55.000 0.00 0.00 0.00 2.17
3162 3364 2.193248 CGAGGCCCCAGAAATCCC 59.807 66.667 0.00 0.00 0.00 3.85
3185 3395 6.876789 CCCTAGTGTAAATTGTATGTGTGTGA 59.123 38.462 0.00 0.00 0.00 3.58
3186 3396 7.389330 CCCTAGTGTAAATTGTATGTGTGTGAA 59.611 37.037 0.00 0.00 0.00 3.18
3305 3540 2.278854 GGCATTCTTGTCTCTCTGCTC 58.721 52.381 0.00 0.00 0.00 4.26
3306 3541 2.093553 GGCATTCTTGTCTCTCTGCTCT 60.094 50.000 0.00 0.00 0.00 4.09
3307 3542 2.931325 GCATTCTTGTCTCTCTGCTCTG 59.069 50.000 0.00 0.00 0.00 3.35
3309 3544 3.657015 TTCTTGTCTCTCTGCTCTGTG 57.343 47.619 0.00 0.00 0.00 3.66
3310 3545 1.271934 TCTTGTCTCTCTGCTCTGTGC 59.728 52.381 0.00 0.00 43.25 4.57
3311 3546 1.273048 CTTGTCTCTCTGCTCTGTGCT 59.727 52.381 3.20 0.00 43.37 4.40
3312 3547 1.336131 TGTCTCTCTGCTCTGTGCTT 58.664 50.000 3.20 0.00 43.37 3.91
3379 3615 6.071320 GGAAATGTTGGCTTCCTATCCTATT 58.929 40.000 0.00 0.00 38.48 1.73
3388 3624 3.360740 TCCTATCCTATTTCCCCAGCA 57.639 47.619 0.00 0.00 0.00 4.41
3410 3646 5.256474 CAAATTCTGGACTAGGAATGGTGT 58.744 41.667 0.00 0.00 33.19 4.16
3411 3647 5.520748 AATTCTGGACTAGGAATGGTGTT 57.479 39.130 0.00 0.00 33.19 3.32
3459 3695 5.365314 CCTCCCTGCCTTCCTCTTATATATC 59.635 48.000 0.00 0.00 0.00 1.63
3535 3773 5.864418 AGCTAGGTCGTGTAAATATTCCA 57.136 39.130 0.00 0.00 0.00 3.53
3586 3832 2.609737 CCGTCGTCTCTGTTAGCCTTTT 60.610 50.000 0.00 0.00 0.00 2.27
3589 3835 4.308265 GTCGTCTCTGTTAGCCTTTTCTT 58.692 43.478 0.00 0.00 0.00 2.52
3596 3842 3.149196 TGTTAGCCTTTTCTTGCTCTGG 58.851 45.455 0.00 0.00 39.00 3.86
3622 3868 0.450583 TGTCTGTCGCTACCACGATC 59.549 55.000 0.00 0.00 45.06 3.69
3623 3869 0.589229 GTCTGTCGCTACCACGATCG 60.589 60.000 14.88 14.88 45.06 3.69
3624 3870 0.741927 TCTGTCGCTACCACGATCGA 60.742 55.000 24.34 0.00 45.06 3.59
3625 3871 0.308068 CTGTCGCTACCACGATCGAT 59.692 55.000 24.34 9.29 45.06 3.59
3626 3872 0.306840 TGTCGCTACCACGATCGATC 59.693 55.000 24.34 15.68 45.06 3.69
3657 3907 1.141881 CTCCCACGAGATGAACGGG 59.858 63.158 0.00 0.00 38.52 5.28
3658 3908 1.304630 TCCCACGAGATGAACGGGA 60.305 57.895 0.00 0.00 43.77 5.14
3694 3944 2.203252 TCCGCCGCCTACGACTAT 60.203 61.111 0.00 0.00 43.93 2.12
3790 4045 0.668535 GTCGCCTCTGCTTTTTGGTT 59.331 50.000 0.00 0.00 34.43 3.67
3801 4056 7.309377 CCTCTGCTTTTTGGTTGATGATCTTAA 60.309 37.037 0.00 0.00 0.00 1.85
3804 4059 8.125978 TGCTTTTTGGTTGATGATCTTAATCT 57.874 30.769 0.00 0.00 32.75 2.40
3854 4109 3.512516 GCTTCATCGGTGGGCTGC 61.513 66.667 0.00 0.00 0.00 5.25
3858 4113 0.611618 TTCATCGGTGGGCTGCAAAT 60.612 50.000 0.50 0.00 0.00 2.32
3965 4223 4.321966 TGCCACCGGTCATGCGAA 62.322 61.111 2.59 0.00 0.00 4.70
3973 4231 0.389296 CGGTCATGCGAACCTGTGTA 60.389 55.000 1.02 0.00 34.45 2.90
3974 4232 1.076332 GGTCATGCGAACCTGTGTAC 58.924 55.000 0.00 0.00 33.78 2.90
3975 4233 1.337823 GGTCATGCGAACCTGTGTACT 60.338 52.381 0.00 0.00 33.78 2.73
3976 4234 1.993370 GTCATGCGAACCTGTGTACTC 59.007 52.381 0.00 0.00 0.00 2.59
3977 4235 1.067142 TCATGCGAACCTGTGTACTCC 60.067 52.381 0.00 0.00 0.00 3.85
3978 4236 1.066858 CATGCGAACCTGTGTACTCCT 60.067 52.381 0.00 0.00 0.00 3.69
3979 4237 0.601558 TGCGAACCTGTGTACTCCTC 59.398 55.000 0.00 0.00 0.00 3.71
4016 4274 9.390795 ACGTACGTTCATGATTATTATCAGTAC 57.609 33.333 16.72 6.01 43.70 2.73
4017 4275 9.608617 CGTACGTTCATGATTATTATCAGTACT 57.391 33.333 7.22 0.00 43.70 2.73
4060 4318 1.839994 CTACAGGCCTGAGAATGGGAA 59.160 52.381 39.19 10.80 0.00 3.97
4103 4361 1.075979 GTTTAGCCGGCGCCATTTTG 61.076 55.000 28.98 9.56 34.57 2.44
4238 4555 2.290367 CGCAGTGAAATGAACAGAACCA 59.710 45.455 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.420306 GTGTTAACATCAAACATCAATGTGCA 59.580 34.615 12.26 0.00 41.61 4.57
30 31 5.616204 GCGGGTGAAAGTAAGTGTTAACATC 60.616 44.000 12.26 3.92 0.00 3.06
31 32 4.214758 GCGGGTGAAAGTAAGTGTTAACAT 59.785 41.667 12.26 0.00 0.00 2.71
32 33 3.560896 GCGGGTGAAAGTAAGTGTTAACA 59.439 43.478 3.59 3.59 0.00 2.41
33 34 3.560896 TGCGGGTGAAAGTAAGTGTTAAC 59.439 43.478 0.00 0.00 0.00 2.01
34 35 3.806380 TGCGGGTGAAAGTAAGTGTTAA 58.194 40.909 0.00 0.00 0.00 2.01
35 36 3.472283 TGCGGGTGAAAGTAAGTGTTA 57.528 42.857 0.00 0.00 0.00 2.41
36 37 2.335316 TGCGGGTGAAAGTAAGTGTT 57.665 45.000 0.00 0.00 0.00 3.32
37 38 2.335316 TTGCGGGTGAAAGTAAGTGT 57.665 45.000 0.00 0.00 0.00 3.55
38 39 3.701532 TTTTGCGGGTGAAAGTAAGTG 57.298 42.857 0.00 0.00 0.00 3.16
102 106 2.037772 AGCTCACGGAGTTCAACAGAAT 59.962 45.455 0.00 0.00 41.61 2.40
163 167 6.043243 AGTCAACCAGAAGAAAGATCTTGGTA 59.957 38.462 13.61 0.00 43.11 3.25
172 180 7.569591 CGCTAAGTTAAGTCAACCAGAAGAAAG 60.570 40.741 0.00 0.00 37.93 2.62
260 276 7.093156 TGTCATATTGTAAAATTTGATGGGGCA 60.093 33.333 2.57 0.00 0.00 5.36
310 326 1.935873 CACCACGGTGCTAATGATGAG 59.064 52.381 2.68 0.00 39.39 2.90
352 368 3.703420 AGGCGAGTTAAGTGTTATAGCG 58.297 45.455 0.00 0.00 0.00 4.26
354 370 7.203910 AGATGAAGGCGAGTTAAGTGTTATAG 58.796 38.462 0.00 0.00 0.00 1.31
355 371 7.108841 AGATGAAGGCGAGTTAAGTGTTATA 57.891 36.000 0.00 0.00 0.00 0.98
386 403 3.243128 CGTGTGCGCTGATTGACA 58.757 55.556 9.73 0.00 0.00 3.58
422 444 7.931407 TCACACTGTGAATAGTAACAAATCACT 59.069 33.333 15.86 0.00 39.78 3.41
480 507 1.063649 GCATGGATCGCACTGCTTG 59.936 57.895 0.00 0.00 0.00 4.01
484 511 3.909776 AATTATGCATGGATCGCACTG 57.090 42.857 10.16 0.00 43.35 3.66
538 565 6.038050 TGAAACTTTTTCCGTACGGTTTATGT 59.962 34.615 32.16 22.33 36.47 2.29
558 585 5.736358 CGCTTCTCTTTATCAGCAATGAAAC 59.264 40.000 0.00 0.00 32.17 2.78
559 586 5.412594 ACGCTTCTCTTTATCAGCAATGAAA 59.587 36.000 0.00 0.00 32.17 2.69
562 589 4.871993 ACGCTTCTCTTTATCAGCAATG 57.128 40.909 0.00 0.00 32.17 2.82
563 590 5.419542 TGTACGCTTCTCTTTATCAGCAAT 58.580 37.500 0.00 0.00 32.17 3.56
564 591 4.816392 TGTACGCTTCTCTTTATCAGCAA 58.184 39.130 0.00 0.00 32.17 3.91
603 665 7.878477 TTAGGAGTACTTAACAAATGTCGTG 57.122 36.000 0.00 0.00 0.00 4.35
633 701 8.448615 GGCGTTCCCATTGTCTAATTATTATAC 58.551 37.037 0.00 0.00 0.00 1.47
644 712 0.981183 TGTAGGCGTTCCCATTGTCT 59.019 50.000 0.00 0.00 35.39 3.41
648 716 2.579410 AACTTGTAGGCGTTCCCATT 57.421 45.000 0.00 0.00 35.39 3.16
657 725 1.477295 ACGCTCCTCTAACTTGTAGGC 59.523 52.381 0.00 0.00 0.00 3.93
662 730 0.809385 TCCGACGCTCCTCTAACTTG 59.191 55.000 0.00 0.00 0.00 3.16
663 731 1.201880 GTTCCGACGCTCCTCTAACTT 59.798 52.381 0.00 0.00 0.00 2.66
665 733 0.522915 CGTTCCGACGCTCCTCTAAC 60.523 60.000 0.00 0.00 43.03 2.34
666 734 1.798735 CGTTCCGACGCTCCTCTAA 59.201 57.895 0.00 0.00 43.03 2.10
667 735 3.494378 CGTTCCGACGCTCCTCTA 58.506 61.111 0.00 0.00 43.03 2.43
684 759 2.544267 ACGACTAAAAAGAGCACACAGC 59.456 45.455 0.00 0.00 46.19 4.40
685 760 4.982916 ACTACGACTAAAAAGAGCACACAG 59.017 41.667 0.00 0.00 0.00 3.66
686 761 4.940463 ACTACGACTAAAAAGAGCACACA 58.060 39.130 0.00 0.00 0.00 3.72
687 762 6.034683 CCATACTACGACTAAAAAGAGCACAC 59.965 42.308 0.00 0.00 0.00 3.82
688 763 6.097356 CCATACTACGACTAAAAAGAGCACA 58.903 40.000 0.00 0.00 0.00 4.57
689 764 5.005490 GCCATACTACGACTAAAAAGAGCAC 59.995 44.000 0.00 0.00 0.00 4.40
690 765 5.107133 GCCATACTACGACTAAAAAGAGCA 58.893 41.667 0.00 0.00 0.00 4.26
691 766 5.107133 TGCCATACTACGACTAAAAAGAGC 58.893 41.667 0.00 0.00 0.00 4.09
692 767 6.588756 TGTTGCCATACTACGACTAAAAAGAG 59.411 38.462 0.00 0.00 0.00 2.85
693 768 6.457355 TGTTGCCATACTACGACTAAAAAGA 58.543 36.000 0.00 0.00 0.00 2.52
694 769 6.367969 ACTGTTGCCATACTACGACTAAAAAG 59.632 38.462 0.00 0.00 0.00 2.27
695 770 6.225318 ACTGTTGCCATACTACGACTAAAAA 58.775 36.000 0.00 0.00 0.00 1.94
696 771 5.786311 ACTGTTGCCATACTACGACTAAAA 58.214 37.500 0.00 0.00 0.00 1.52
697 772 5.395682 ACTGTTGCCATACTACGACTAAA 57.604 39.130 0.00 0.00 0.00 1.85
698 773 5.449588 GCTACTGTTGCCATACTACGACTAA 60.450 44.000 2.72 0.00 0.00 2.24
699 774 4.036027 GCTACTGTTGCCATACTACGACTA 59.964 45.833 2.72 0.00 0.00 2.59
700 775 3.181489 GCTACTGTTGCCATACTACGACT 60.181 47.826 2.72 0.00 0.00 4.18
701 776 3.114065 GCTACTGTTGCCATACTACGAC 58.886 50.000 2.72 0.00 0.00 4.34
702 777 3.431922 GCTACTGTTGCCATACTACGA 57.568 47.619 2.72 0.00 0.00 3.43
712 787 0.237498 GTTCGGTTGGCTACTGTTGC 59.763 55.000 5.65 5.65 34.56 4.17
713 788 0.511221 CGTTCGGTTGGCTACTGTTG 59.489 55.000 7.76 0.00 34.56 3.33
714 789 0.601841 CCGTTCGGTTGGCTACTGTT 60.602 55.000 7.76 0.00 34.56 3.16
715 790 1.005394 CCGTTCGGTTGGCTACTGT 60.005 57.895 7.76 0.00 34.56 3.55
716 791 0.736325 CTCCGTTCGGTTGGCTACTG 60.736 60.000 11.04 1.17 34.20 2.74
717 792 0.896940 TCTCCGTTCGGTTGGCTACT 60.897 55.000 11.04 0.00 0.00 2.57
718 793 0.175073 ATCTCCGTTCGGTTGGCTAC 59.825 55.000 11.04 0.00 0.00 3.58
719 794 0.458669 GATCTCCGTTCGGTTGGCTA 59.541 55.000 11.04 0.00 0.00 3.93
720 795 1.218316 GATCTCCGTTCGGTTGGCT 59.782 57.895 11.04 0.00 0.00 4.75
721 796 1.814169 GGATCTCCGTTCGGTTGGC 60.814 63.158 11.04 0.77 0.00 4.52
727 802 2.893637 ACTCAAATGGATCTCCGTTCG 58.106 47.619 4.20 0.00 44.07 3.95
734 809 5.449553 GGGGTCAAATACTCAAATGGATCT 58.550 41.667 0.00 0.00 0.00 2.75
762 837 0.102300 GCTCGGAGGCTCTCTCTTTC 59.898 60.000 15.23 0.00 42.10 2.62
764 839 1.000270 TGCTCGGAGGCTCTCTCTT 60.000 57.895 15.23 0.00 42.10 2.85
779 854 0.979665 TAAAGGTGCTCTGCTCTGCT 59.020 50.000 0.00 0.00 0.00 4.24
780 855 2.035530 ATAAAGGTGCTCTGCTCTGC 57.964 50.000 0.00 0.00 0.00 4.26
781 856 4.764172 AGTTATAAAGGTGCTCTGCTCTG 58.236 43.478 0.00 0.00 0.00 3.35
782 857 4.141824 GGAGTTATAAAGGTGCTCTGCTCT 60.142 45.833 0.00 0.00 0.00 4.09
783 858 4.123506 GGAGTTATAAAGGTGCTCTGCTC 58.876 47.826 0.00 0.00 0.00 4.26
827 906 4.649705 TGGGGTTGGAGGAGCGGA 62.650 66.667 0.00 0.00 0.00 5.54
868 947 3.933542 GAGGAGCTGGGACTGGGGT 62.934 68.421 0.00 0.00 0.00 4.95
957 1042 2.583520 CCCTCTCTGTCTGGCTGC 59.416 66.667 0.00 0.00 0.00 5.25
958 1043 2.583520 GCCCTCTCTGTCTGGCTG 59.416 66.667 0.00 0.00 40.77 4.85
965 1050 2.284258 AGCTTCCGCCCTCTCTGT 60.284 61.111 0.00 0.00 36.60 3.41
1635 1732 2.363683 CTCACCTCTTTCTTCATGGCC 58.636 52.381 0.00 0.00 0.00 5.36
1714 1816 3.190535 ACGGAAATGTAACATGGCAAGTC 59.809 43.478 0.00 0.00 0.00 3.01
1783 1890 3.546543 CCTAATCGGGCCGGAGCA 61.547 66.667 27.98 6.84 42.56 4.26
1832 1939 2.486966 GGCGAGCTGGTGATTTGC 59.513 61.111 0.00 0.00 0.00 3.68
1863 1970 1.896660 GCTGTTTGTTGCGGGAGGA 60.897 57.895 0.00 0.00 0.00 3.71
1870 1977 1.791103 TACGGCCTGCTGTTTGTTGC 61.791 55.000 9.17 0.00 36.80 4.17
1948 2059 4.532314 TTCTCTTACTCCCTTTCGGTTC 57.468 45.455 0.00 0.00 0.00 3.62
2006 2118 2.095461 GGGCAAAGAAAGATCCACTCC 58.905 52.381 0.00 0.00 0.00 3.85
2026 2138 1.133025 GATCATTCACCGCCCAAACAG 59.867 52.381 0.00 0.00 0.00 3.16
2139 2251 2.189191 GAGCTGGTGATGCAGTGGGA 62.189 60.000 0.00 0.00 0.00 4.37
2140 2252 1.748122 GAGCTGGTGATGCAGTGGG 60.748 63.158 0.00 0.00 0.00 4.61
2141 2253 2.104859 CGAGCTGGTGATGCAGTGG 61.105 63.158 0.00 0.00 0.00 4.00
2142 2254 1.375140 ACGAGCTGGTGATGCAGTG 60.375 57.895 0.00 0.00 0.00 3.66
2143 2255 1.375140 CACGAGCTGGTGATGCAGT 60.375 57.895 23.05 0.00 40.38 4.40
2144 2256 2.104859 CCACGAGCTGGTGATGCAG 61.105 63.158 28.17 8.87 40.38 4.41
2145 2257 2.046988 CCACGAGCTGGTGATGCA 60.047 61.111 28.17 0.00 40.38 3.96
2152 2264 2.126071 CCACGTACCACGAGCTGG 60.126 66.667 5.61 0.00 46.05 4.85
2153 2265 2.126071 CCCACGTACCACGAGCTG 60.126 66.667 5.61 0.00 46.05 4.24
2154 2266 4.065281 GCCCACGTACCACGAGCT 62.065 66.667 5.61 0.00 46.05 4.09
2171 2283 1.596954 CCAACAAAGCGAAGTGGAACG 60.597 52.381 0.00 0.00 45.86 3.95
2172 2284 1.404035 ACCAACAAAGCGAAGTGGAAC 59.596 47.619 0.00 0.00 0.00 3.62
2173 2285 1.757682 ACCAACAAAGCGAAGTGGAA 58.242 45.000 0.00 0.00 0.00 3.53
2212 2324 3.453679 GAAGGACGGAGCCGAGCT 61.454 66.667 16.83 0.00 43.88 4.09
2286 2404 2.225522 TGGAATGGACAGAGGAGGTGTA 60.226 50.000 0.00 0.00 0.00 2.90
2287 2405 1.280457 GGAATGGACAGAGGAGGTGT 58.720 55.000 0.00 0.00 0.00 4.16
2289 2407 2.122768 GATGGAATGGACAGAGGAGGT 58.877 52.381 0.00 0.00 0.00 3.85
2290 2408 2.121948 TGATGGAATGGACAGAGGAGG 58.878 52.381 0.00 0.00 0.00 4.30
2297 2415 2.683447 CGGGTGAATGATGGAATGGACA 60.683 50.000 0.00 0.00 0.00 4.02
2302 2420 2.126882 TCTCCGGGTGAATGATGGAAT 58.873 47.619 0.00 0.00 0.00 3.01
2304 2422 1.209504 GTTCTCCGGGTGAATGATGGA 59.790 52.381 14.04 0.00 0.00 3.41
2323 2444 0.530211 GCGAGATGCAGATGCTCTGT 60.530 55.000 6.35 0.00 45.94 3.41
2404 2542 1.206371 CCCCTTCTACCACTAACACCG 59.794 57.143 0.00 0.00 0.00 4.94
2405 2543 1.558294 CCCCCTTCTACCACTAACACC 59.442 57.143 0.00 0.00 0.00 4.16
2406 2544 1.065636 GCCCCCTTCTACCACTAACAC 60.066 57.143 0.00 0.00 0.00 3.32
2407 2545 1.203389 AGCCCCCTTCTACCACTAACA 60.203 52.381 0.00 0.00 0.00 2.41
2408 2546 1.209747 CAGCCCCCTTCTACCACTAAC 59.790 57.143 0.00 0.00 0.00 2.34
2409 2547 1.580059 CAGCCCCCTTCTACCACTAA 58.420 55.000 0.00 0.00 0.00 2.24
2410 2548 0.981277 GCAGCCCCCTTCTACCACTA 60.981 60.000 0.00 0.00 0.00 2.74
2411 2549 2.301738 GCAGCCCCCTTCTACCACT 61.302 63.158 0.00 0.00 0.00 4.00
2412 2550 2.272471 GCAGCCCCCTTCTACCAC 59.728 66.667 0.00 0.00 0.00 4.16
2413 2551 3.015145 GGCAGCCCCCTTCTACCA 61.015 66.667 0.00 0.00 0.00 3.25
2414 2552 2.309504 AAGGCAGCCCCCTTCTACC 61.310 63.158 8.22 0.00 41.28 3.18
2415 2553 3.416351 AAGGCAGCCCCCTTCTAC 58.584 61.111 8.22 0.00 41.28 2.59
2465 2606 6.732896 TGATTCCTTCCAATCTAGGAGTAC 57.267 41.667 0.00 0.00 41.38 2.73
2685 2856 1.681538 ATCGTACTCGCCTGTCATCT 58.318 50.000 0.00 0.00 36.96 2.90
2688 2859 0.098200 CGAATCGTACTCGCCTGTCA 59.902 55.000 0.00 0.00 36.96 3.58
2689 2860 0.591741 CCGAATCGTACTCGCCTGTC 60.592 60.000 0.82 0.00 34.95 3.51
2690 2861 1.028330 TCCGAATCGTACTCGCCTGT 61.028 55.000 0.82 0.00 34.95 4.00
2691 2862 0.099968 TTCCGAATCGTACTCGCCTG 59.900 55.000 0.82 0.00 34.95 4.85
2692 2863 1.030457 ATTCCGAATCGTACTCGCCT 58.970 50.000 0.82 0.00 34.95 5.52
2693 2864 1.129326 CATTCCGAATCGTACTCGCC 58.871 55.000 0.82 0.00 34.95 5.54
2694 2865 2.044860 CTCATTCCGAATCGTACTCGC 58.955 52.381 0.82 0.00 34.95 5.03
2698 2869 3.187700 ACAAGCTCATTCCGAATCGTAC 58.812 45.455 0.82 0.00 0.00 3.67
2699 2870 3.520290 ACAAGCTCATTCCGAATCGTA 57.480 42.857 0.82 0.00 0.00 3.43
2715 2886 9.085250 CAGCTATACAATGATCAGCTATACAAG 57.915 37.037 0.09 0.00 40.50 3.16
2717 2888 8.353423 TCAGCTATACAATGATCAGCTATACA 57.647 34.615 0.09 0.00 40.50 2.29
2718 2889 9.462174 GATCAGCTATACAATGATCAGCTATAC 57.538 37.037 0.09 0.00 45.59 1.47
2726 2897 6.198029 CGATTCGGATCAGCTATACAATGATC 59.802 42.308 4.19 5.97 45.57 2.92
2727 2898 6.038985 CGATTCGGATCAGCTATACAATGAT 58.961 40.000 4.19 0.00 36.40 2.45
2728 2899 5.402398 CGATTCGGATCAGCTATACAATGA 58.598 41.667 4.19 0.00 32.33 2.57
2729 2900 4.032217 GCGATTCGGATCAGCTATACAATG 59.968 45.833 8.34 0.00 32.68 2.82
2730 2901 4.081972 AGCGATTCGGATCAGCTATACAAT 60.082 41.667 17.70 0.00 39.01 2.71
2731 2902 3.255888 AGCGATTCGGATCAGCTATACAA 59.744 43.478 17.70 0.00 39.01 2.41
2732 2903 2.820197 AGCGATTCGGATCAGCTATACA 59.180 45.455 17.70 0.00 39.01 2.29
2751 2922 1.671880 GAAACCGCGACACGTAGAGC 61.672 60.000 8.23 0.00 41.42 4.09
2752 2923 0.386352 TGAAACCGCGACACGTAGAG 60.386 55.000 8.23 0.00 41.42 2.43
2801 2972 3.587797 ACAAGCTCATGATTTTGCAGG 57.412 42.857 15.46 6.63 0.00 4.85
2858 3030 2.727798 GCAGTACGTTAAGTTGAGCGAA 59.272 45.455 0.00 0.00 0.00 4.70
2860 3032 2.325761 AGCAGTACGTTAAGTTGAGCG 58.674 47.619 0.00 0.00 0.00 5.03
2864 3036 7.945326 GTACTAGTAGCAGTACGTTAAGTTG 57.055 40.000 1.87 0.00 40.98 3.16
2882 3054 7.774157 TCATCAGGACTAAACTACCAGTACTAG 59.226 40.741 0.00 0.00 33.49 2.57
2888 3064 4.466370 TGGTCATCAGGACTAAACTACCAG 59.534 45.833 0.00 0.00 46.16 4.00
2964 3140 1.774639 GCAATGGCTGGCGATAATTG 58.225 50.000 7.39 7.39 36.96 2.32
2977 3175 2.574450 ACCAAAAGGCAAAAGCAATGG 58.426 42.857 0.00 0.00 0.00 3.16
2981 3179 2.102252 CCTGTACCAAAAGGCAAAAGCA 59.898 45.455 0.00 0.00 0.00 3.91
3160 3362 6.876789 TCACACACATACAATTTACACTAGGG 59.123 38.462 0.00 0.00 0.00 3.53
3162 3364 9.973246 GATTCACACACATACAATTTACACTAG 57.027 33.333 0.00 0.00 0.00 2.57
3185 3395 3.883830 AGAGCAAGACGATGTGAGATT 57.116 42.857 0.00 0.00 0.00 2.40
3186 3396 3.883830 AAGAGCAAGACGATGTGAGAT 57.116 42.857 0.00 0.00 0.00 2.75
3388 3624 5.520748 ACACCATTCCTAGTCCAGAATTT 57.479 39.130 0.00 0.00 30.29 1.82
3405 3641 1.601903 GTCGTTGCTTCATGAACACCA 59.398 47.619 3.38 0.00 0.00 4.17
3410 3646 3.476552 AGAAAGGTCGTTGCTTCATGAA 58.523 40.909 8.12 8.12 0.00 2.57
3411 3647 3.067106 GAGAAAGGTCGTTGCTTCATGA 58.933 45.455 0.00 0.00 0.00 3.07
3459 3695 3.604065 TCTCGTTATGCTAGTGCTACG 57.396 47.619 0.00 0.00 40.48 3.51
3500 3736 5.526479 CACGACCTAGCTAAGTACAGTGATA 59.474 44.000 14.91 0.00 0.00 2.15
3535 3773 3.736433 CGCAGTCACTAGATTAAGCAGCT 60.736 47.826 0.00 0.00 0.00 4.24
3586 3832 2.092429 AGACACAAAACCCAGAGCAAGA 60.092 45.455 0.00 0.00 0.00 3.02
3589 3835 1.064758 ACAGACACAAAACCCAGAGCA 60.065 47.619 0.00 0.00 0.00 4.26
3596 3842 1.529865 GGTAGCGACAGACACAAAACC 59.470 52.381 0.00 0.00 0.00 3.27
3622 3868 1.269309 GGAGATCACCGGTCAAGATCG 60.269 57.143 21.34 3.95 42.21 3.69
3623 3869 1.069358 GGGAGATCACCGGTCAAGATC 59.931 57.143 20.47 20.47 38.70 2.75
3624 3870 1.123928 GGGAGATCACCGGTCAAGAT 58.876 55.000 2.59 4.49 0.00 2.40
3625 3871 0.252057 TGGGAGATCACCGGTCAAGA 60.252 55.000 2.59 0.00 0.00 3.02
3626 3872 0.108138 GTGGGAGATCACCGGTCAAG 60.108 60.000 2.59 0.00 0.00 3.02
3657 3907 0.706729 CGGCTCGTGAAACTACGTTC 59.293 55.000 0.00 0.00 44.06 3.95
3658 3908 0.031178 ACGGCTCGTGAAACTACGTT 59.969 50.000 0.00 0.00 44.06 3.99
3694 3944 2.966732 GCTCCCGTTCACATCCCCA 61.967 63.158 0.00 0.00 0.00 4.96
3790 4045 7.224753 GCGGTTCACTTTAGATTAAGATCATCA 59.775 37.037 0.00 0.00 34.60 3.07
3801 4056 1.734707 CGGACGCGGTTCACTTTAGAT 60.735 52.381 12.47 0.00 0.00 1.98
3804 4059 0.664166 GACGGACGCGGTTCACTTTA 60.664 55.000 12.47 0.00 0.00 1.85
3854 4109 7.976135 ATCATCCTCTTATCCGAAAGATTTG 57.024 36.000 0.00 0.00 35.04 2.32
3858 4113 6.495181 AGCTAATCATCCTCTTATCCGAAAGA 59.505 38.462 0.00 0.00 34.39 2.52
3943 4201 3.731728 ATGACCGGTGGCAGGCAT 61.732 61.111 14.63 4.81 0.00 4.40
3962 4220 1.546961 AGGAGGAGTACACAGGTTCG 58.453 55.000 0.00 0.00 0.00 3.95
3965 4223 3.833070 CTGTTAAGGAGGAGTACACAGGT 59.167 47.826 0.00 0.00 0.00 4.00
3979 4237 2.030007 TGAACGTACGTCCCTGTTAAGG 60.030 50.000 23.05 0.00 44.06 2.69
4016 4274 7.480810 AGTGTGTTGTAGGCTTAAAAAGAAAG 58.519 34.615 0.00 0.00 0.00 2.62
4017 4275 7.399245 AGTGTGTTGTAGGCTTAAAAAGAAA 57.601 32.000 0.00 0.00 0.00 2.52
4022 4280 5.761234 CCTGTAGTGTGTTGTAGGCTTAAAA 59.239 40.000 0.00 0.00 0.00 1.52
4026 4284 2.550208 GCCTGTAGTGTGTTGTAGGCTT 60.550 50.000 0.00 0.00 45.44 4.35
4027 4285 1.002087 GCCTGTAGTGTGTTGTAGGCT 59.998 52.381 0.00 0.00 45.44 4.58
4086 4344 2.881389 CAAAATGGCGCCGGCTAA 59.119 55.556 26.68 10.20 39.81 3.09
4117 4375 4.941873 ACCTTCGAACAAGATTTGGATACC 59.058 41.667 0.00 0.00 34.12 2.73
4123 4381 4.776743 CAGTCACCTTCGAACAAGATTTG 58.223 43.478 0.00 0.00 0.00 2.32
4154 4412 1.154205 GCCCACAGATGAATCGACGG 61.154 60.000 0.00 0.00 0.00 4.79
4160 4418 5.010012 GGAATATTTTCGCCCACAGATGAAT 59.990 40.000 0.00 0.00 32.28 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.